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- PDB-6l10: PHF20L1 Tudor1 - MES -

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Basic information

Entry
Database: PDB / ID: 6l10
TitlePHF20L1 Tudor1 - MES
ComponentsPHD finger protein 20-like protein 1
KeywordsMETAL BINDING PROTEIN / PHF20L1 / Tudor / MES
Function / homology
Function and homology information


methylation-dependent protein binding / NSL complex / Formation of WDR5-containing histone-modifying complexes / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein catabolic process / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm
Similarity search - Function
: / PHD finger protein 20-like protein 1 / PHD finger protein 20-like / Agenet domain, plant type / Tudor-like domain present in plant sequences. / PhD finger domain / mbt repeat / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain ...: / PHD finger protein 20-like protein 1 / PHD finger protein 20-like / Agenet domain, plant type / Tudor-like domain present in plant sequences. / PhD finger domain / mbt repeat / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
PHD finger protein 20-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLv, M.Q. / Gao, J.
CitationJournal: J Phys Chem Lett / Year: 2020
Title: Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1.
Authors: Lv, M. / Gao, J. / Li, M. / Ma, R. / Li, F. / Liu, Y. / Liu, M. / Zhang, J. / Yao, X. / Wu, J. / Shi, Y. / Tang, Y. / Pan, Y. / Zhang, Z. / Ruan, K.
History
DepositionSep 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 20-like protein 1
B: PHD finger protein 20-like protein 1
C: PHD finger protein 20-like protein 1
D: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,94012
Polymers34,7754
Non-polymers1,1658
Water3,981221
1
A: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9853
Polymers8,6941
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4930 Å2
MethodPISA
2
B: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9853
Polymers8,6941
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4720 Å2
MethodPISA
3
C: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8892
Polymers8,6941
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4440 Å2
MethodPISA
4
D: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0814
Polymers8,6941
Non-polymers3873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area4810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.175, 52.773, 101.375
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PHD finger protein 20-like protein 1 / Plant Homeodomain (PHD) Finger Protein 20-like 1


Mass: 8693.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF20L1, CGI-72 / Production host: Escherichia coli (E. coli) / References: UniProt: A8MW92
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 8000, 0.2M (NH4)2SO4, 0.1mM MES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→37.103 Å / Num. obs: 38337 / % possible obs: 99.78 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 24.8
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3702 / Rsym value: 0.42

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Processing

Software
NameVersionClassification
PHENIX3.3.22refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SD4

3sd4


Resolution: 1.6→37.103 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 2.07 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2209 1897 5.04 %
Rwork0.1941 35718 -
obs0.1955 37615 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.35 Å2 / Biso mean: 22.6573 Å2 / Biso min: 7.18 Å2
Refinement stepCycle: final / Resolution: 1.6→37.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 68 221 2653
Biso mean--43.81 25.79 -
Num. residues----275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.640.22391340.20012487100
1.64-1.68440.2441390.20432540100
1.6844-1.73390.25351230.20722509100
1.7339-1.78990.23321490.20042505100
1.7899-1.85390.2331300.19442522100
1.8539-1.92810.22991170.19152551100
1.9281-2.01580.21021200.20252550100
2.0158-2.12210.25031140.19422553100
2.1221-2.2550.21711440.19862530100
2.255-2.42910.21941250.20052560100
2.4291-2.67350.23211510.21012547100
2.6735-3.06020.24331750.2052539100
3.0602-3.85490.1991310.18532607100
3.8549-37.1030.19821450.1768271899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.53450.1749-0.78790.99090.34572.48620.12510.15220.0377-0.0521-0.00760.1169-0.2141-0.4445-0.07060.10770.03540.01060.13980.01960.11284.1884-8.422238.3159
21.28180.0482-0.85921.50030.73972.88630.0102-0.02910.0290.01070.0626-0.2001-0.09230.2801-0.03050.07210.0165-0.01350.0967-0.01210.124822.361-9.832412.2667
32.79280.46841.29272.544-0.7662.672-0.01220.2883-0.246-0.26710.0235-0.24330.35250.19040.0140.13-0.00970.02830.1216-0.02250.126929.8897-9.167938.0472
42.7315-0.78130.85042.08890.40033.1729-0.082-0.1467-0.31260.26880.06670.17610.3744-0.11680.00230.13520.00710.02940.09280.00090.1287-3.3583-8.317712.7618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 70)A1 - 70
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 70)B1 - 70
3X-RAY DIFFRACTION3(chain 'C' and resid 4 through 70)C4 - 70
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 70)D3 - 70

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